Viatoolbox -

| Option | Description | |--------|-------------| | -i , --input | FASTQ file (supports .gz) | | -r , --refindex | Path to pre-built indices | | -o , --outdir | Output directory | | --min-mapq | Minimum mapping quality (default 30) | | --max-insert | Max fragment length for paired-end (default 800) | | --threads | CPU threads |

| Option | Description | |--------|-------------| | -r , --ref | Reference genome FASTA | | -v , --vector | Vector sequence FASTA | | -o , --outdir | Output directory for indices | | --bwa | Use BWA-MEM (default) | Main integration site detection. viatoolbox